[CP2K:2142] Cell size problem
Laino Teodoro
teodor... at gmail.com
Thu Jun 25 21:25:03 UTC 2009
Very probably it is an allocation problem (running out of memory).
To be sure you should post more info. For example, in the working
directory there should be
several *localLog* files. The content of one of them would be helpful..
Teo
On 25 Jun 2009, at 22:49, roberto wrote:
>
> I have perfomed a WF optimization of a little peptide in vacuo without
> problem.
> If I try to increase the size of the cell (from 35x35x35 to 40x40x40),
> the simulation fail.
> I post the inputfile and follow the output error message.
>
> Thanks for any suggestion.
>
>
> ## INPUT ##
> &FORCE_EVAL
> METHOD Quickstep
> &DFT
> &POISSON
> PERIODIC NONE
> POISSON_SOLVER MT
> &END POISSON
> CHARGE +1
> &MGRID
> CUTOFF 280
> &END MGRID
> &QS
> EPS_DEFAULT 1.0E-8
> &END QS
> &SCF
> &OT
> PRECONDITIONER FULL_SINGLE_INVERSE
> &END OT
> MAX_SCF 40
> &OUTER_SCF
> MAX_SCF 5
> &END OUTER_SCF
> &END SCF
> &XC
> &XC_FUNCTIONAL BLYP
> &END XC_FUNCTIONAL
> &END XC
> &END DFT
> &SUBSYS
> &CELL
> PERIODIC NONE
> ABC 40.0 40.0 40.0
> UNIT ANGSTROM
> &END CELL
> &COORD
> N 11.4324736309 -6.1371572063 10.1357218931
> H 11.1948075937 -6.8906101345 10.7821924672
> H 10.9381862969 -6.3405541515 9.2632495044
> C 10.9499715702 -4.8402675750 10.6521973274
> H 11.3386245365 -4.7296425589 11.6677585473
> C 11.4913131810 -3.6752836914 9.7832152944
> H 11.2516744925 -3.8960378486 8.7344971467
> H 10.9285010983 -2.7702123308 10.0417793494
> C 12.9962124352 -3.4081941284 9.9438576821
> H 13.2545611858 -3.3414422460 11.0083607468
> H 13.5793843176 -4.2349628942 9.5244606629
> C 13.4276150724 -2.0986464686 9.2465939026
> H 14.5097616796 -1.9519749811 9.3487493765
> H 13.1879571320 -2.1284201500 8.1783151066
> N 12.7146699325 -0.9515928240 9.8558121776
> H 12.5828552979 -1.0107633654 10.8919178425
> C 12.1135559906 0.0441274020 9.2139901029
> N 12.4394518112 0.3403191250 7.9167217260
> H 13.4354822732 0.3681036873 7.7191911152
> H 11.9329746051 1.1211570509 7.5131991344
> N 11.1218376294 0.7371180721 9.8136134969
> H 10.8845997299 0.4742930918 10.7753580754
> H 11.0626157210 1.7370925590 9.6197738858
> C 9.4085853225 -4.6963484515 10.6225043190
> O 8.7929578553 -4.9975325132 9.5903800315
> N 8.7856778560 -4.1441412798 11.7203597433
> C 7.3486285567 -3.8102551517 11.7099480717
> H 6.8197192907 -4.5278210668 11.0766326891
> C 6.9582417964 -3.9259460918 13.2069269204
> H 6.0748168733 -3.3358993177 13.4681026699
> H 6.7441098192 -4.9759288944 13.4343207792
> C 8.2282987207 -3.4419031893 13.9424055935
> H 8.2310874957 -2.3492127686 13.9975911707
> H 8.2955580201 -3.8288025246 14.9625954573
> C 9.4034512549 -3.9235517293 13.0609426956
> H 10.2003124860 -3.1759063533 13.0064126519
> H 9.8280374116 -4.8622782613 13.4349980596
> C 7.1101286450 -2.3801594356 11.1412507028
> O 8.0203520380 -1.5310504742 11.0477720011
> N 5.8392674941 -2.0823894794 10.7205335448
> C 5.6355139703 -0.8941970496 9.8616586631
> H 6.4068582242 -0.9016299355 9.0817309576
> C 4.2200778144 -1.1170421588 9.2549104403
> H 3.7003760394 -0.1719620880 9.0653987172
> H 4.3221404500 -1.6430084891 8.2982109770
> C 3.4941370231 -2.0064473870 10.2877472021
> H 3.0786537890 -1.3852707278 11.0878641139
> H 2.6836333737 -2.5921705326 9.8413944307
> C 4.6079587796 -2.9171615522 10.8501847587
> H 4.4363094156 -3.1758339663 11.8977183292
> H 4.7026866900 -3.8463230114 10.2747817658
> C 5.7458899497 0.4525397791 10.6137692543
> O 5.2154503855 0.7039309036 11.7192531172
> N 6.4344225918 1.3948594344 9.9368461571
> H 6.9322429528 1.1986520759 9.0691552019
> C 6.5700409770 2.7589843070 10.4088570300
> H 5.5947332208 3.1651635665 10.6980024914
> H 7.2187935767 2.8031426981 11.2970319085
> C 7.2295977003 3.5687623281 9.2776439289
> O 7.7340229907 2.9845949290 8.3112331112
> N 7.2238485090 4.9191972013 9.5096174983
> H 6.6972441974 5.2437226270 10.3188538415
> C 7.9461520189 5.9673404267 8.7653679704
> H 8.0948922681 5.6108506893 7.7422282223
> C 7.1259847303 7.2983111829 8.7421278471
> H 7.7166350535 8.0185624933 8.1702963661
> H 6.1954232051 7.1154799216 8.1942654314
> C 6.8262531031 7.8236225973 10.1409243252
> C 7.8009125294 8.5254653877 10.8745041594
> H 8.7512326191 8.7682386096 10.4069719956
> C 5.5931262870 7.5527765173 10.7617727760
> H 4.7994354740 7.0694296050 10.1946741872
> C 7.5588299749 8.9164837495 12.1941172113
> H 8.3165010987 9.4774015857 12.7357860474
> C 5.3567146254 7.9306360270 12.0896783873
> H 4.3996280301 7.7066013719 12.5536143802
> C 6.3440138894 8.6051885011 12.8127723611
> H 6.1632870999 8.8990656943 13.8430462390
> C 9.3571813479 6.2746847214 9.3428304585
> O 10.0791474867 7.1283336115 8.8105336198
> N 9.6823888175 5.6087213903 10.4868666966
> H 9.1151350681 4.8239948493 10.7846719438
> C 11.0098655520 5.6810980820 11.0893328531
> H 11.3426585696 6.7203820495 11.0590121012
> C 10.9201366090 5.2066006718 12.5630668632
> H 11.9200185517 5.1756653398 13.0151902147
> H 10.3015773371 5.9179548033 13.1188135468
> O 10.2584835828 3.9285493471 12.6795126544
> H 10.8564137049 3.2408538678 12.3296344025
> C 11.9591884550 4.7647976442 10.3069677329
> O 11.6296147202 3.5817188030 10.0708465781
> N 13.1788137378 5.2443511260 9.9396802843
> C 14.0563338490 4.4032200505 9.0829530013
> H 13.4719025368 4.0064794776 8.2494747614
> C 15.1397054888 5.3960392482 8.5730358684
> H 16.1203110935 4.9234846486 8.4844687895
> H 14.8553721417 5.7493278524 7.5765557887
> C 15.1264756032 6.5643344145 9.5850212352
> H 15.7735259998 6.3373775806 10.4394603902
> H 15.4728307826 7.5034783310 9.1434240480
> C 13.6595469021 6.6572283699 10.0451222428
> H 13.5728058669 7.0165901585 11.0727973352
> H 13.0585342596 7.3015141176 9.3943770370
> C 14.6014154503 3.1332153934 9.7817732244
> O 14.7387246309 2.1025043414 9.1057259732
> N 14.9321391220 3.2469089599 11.1089829812
> H 14.5620137473 4.0402574483 11.6282916218
> C 15.3192535703 2.1011402694 11.9474204093
> H 15.0780360517 1.2020681276 11.3732515255
> C 16.8585665040 2.0994231406 12.2382822730
> H 17.3539614068 2.1958403990 11.2643638601
> H 17.1082296466 2.9955427380 12.8181669038
> C 17.3697857804 0.8568138702 12.9524885282
> C 17.3797137994 -0.3930013796 12.3059460314
> H 17.0418999476 -0.4717813269 11.2744331783
> C 17.8502344440 0.9299228647 14.2688436131
> H 17.8584539601 1.8877312361 14.7838482599
> C 17.8431707860 -1.5357637564 12.9659077610
> H 17.8448134688 -2.4938071540 12.4526028964
> C 18.3280162135 -0.2086287981 14.9255393119
> H 18.7080035730 -0.1258151027 15.9403383929
> C 18.3199824362 -1.4468283157 14.2780028322
> H 18.6875105233 -2.3333511257 14.7873511883
> C 14.4291885252 2.1139040343 13.2372349862
> O 13.8712375863 3.1460055627 13.6428990047
> N 14.3252227703 0.8875480108 13.8432137400
> H 14.8187807167 0.1440451701 13.3544501520
> C 13.0771550709 0.3363039184 14.4658453947
> H 13.4083046903 -0.5658317525 14.9919599824
> C 12.3866081840 1.2690277101 15.4739897598
> H 13.1573362728 1.6845612875 16.1305225542
> H 11.9429043004 2.1192890169 14.9506741542
> C 11.3196142795 0.5168432069 16.3320382507
> H 11.2988399674 -0.5507043523 16.0745237971
> H 11.5970777966 0.5648971423 17.3905058535
> C 9.8816633280 1.0607292795 16.2237239485
> H 9.2322412111 0.5053361766 16.9120837269
> H 9.8604573253 2.1217563077 16.5141963374
> N 9.3703250501 0.8983805551 14.8491982364
> H 10.0820115597 0.7932029452 14.0786879557
> C 8.0864971754 0.8564153995 14.5080177069
> N 7.1078801829 1.1398390529 15.4161841516
> H 7.3261229183 1.6921520704 16.2346043529
> H 6.1392249660 1.1152097272 15.1215765008
> N 7.7231598143 0.5099811222 13.2596078532
> H 6.7554425343 0.5884413276 12.9348072587
> H 8.3607775713 0.0058338362 12.6465521841
> C 12.2320591043 -0.1584710118 13.2320032792
> O 12.7682553788 -1.1027541201 12.5820166002
> O 11.1533115804 0.4532114808 12.9004593689
> &END COORD
> &KIND H
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q1
> &END KIND
> &KIND C
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q4
> &END KIND
> &KIND N
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q5
> &END KIND
> &KIND O
> BASIS_SET TZV2P-GTH
> POTENTIAL GTH-BLYP-q6
> &END KIND
> &END SUBSYS
> &END FORCE_EVAL
>
> &MOTION
> &GEO_OPT
> OPTIMIZER LBFGS
> MAX_ITER 100
> &CG
> MAX_STEEP_STEPS 5
> &LINE_SEARCH
> TYPE 2PNT
> &END LINE_SEARCH
> &END CG
> &END GEO_OPT
>
> &MD
> ENSEMBLE NVT
> STEPS 50000
> TIMESTEP 1.0
> TEMPERATURE 50.0
> &END MD
>
> &PRINT
> &FORCES
> FORMAT XMOL
> &EACH
> MD 1
> &END EACH
> &END FORCES
> &END PRINT
> &END MOTION
>
> &GLOBAL
> PROJECT 6
> RUN_TYPE WFN_OPT
> PRINT_LEVEL LOW
> &END GLOBAL
>
> ############################################
> CP2K| version string: CP2K version 2.0.0 (Development
> Version)
> CP2K| is freely available from http://
> cp2k.berlios.de/
> CP2K| Program compiled at Thu Apr 24 00:52:50
> CEST 2008
> CP2K| Program compiled
> on node1309
> CP2K| Program compiled for Linux-
> x86-64-intel
> CP2K| Last CVS
> entry
> CP2K| Input file name
> prot_6_2103.inp
>
> GLOBAL| Force Environment
> number 1
> GLOBAL| Basis set file name
> BASIS_SET
> GLOBAL| Potential file name
> POTENTIAL
> GLOBAL| MM Potential file name
> MM_POTENTIAL
> GLOBAL| Coordinate file name
> __STD_INPUT__
> GLOBAL| Method
> name CP2K
> GLOBAL| Project
> name 6
> GLOBAL| Preferred FFT
> library FFTW2
> GLOBAL| Run
> type ENERGY
> GLOBAL| All-to-all communication in single
> precision F
> GLOBAL| FFTs using library dependent
> lengths F
> GLOBAL| Global print
> level 1
> GLOBAL| Total number of message passing
> processes 16
> GLOBAL| Number of threads for this
> process 1
> GLOBAL| This output is from
> process 0
>
>
> GENERATE| Preliminary Number of Bonds
> generated: 0
> GENERATE| Achieved consistency in connectivity generation.
> GENERATE| Number of Bonds
> generated: 0
> GENERATE| Preliminary Number of Bends
> generated: 0
> GENERATE| Number of Bends
> generated: 0
> GENERATE| Number of UB
> generated: 0
> GENERATE| Preliminary Number of Torsions
> generated: 0
> GENERATE| Number of Torsions
> generated: 0
> GENERATE| Number of Impropers
> generated: 0
> GENERATE| Number of 1-4 interactions
> generated: 0
>
>
> **********************************************************************
> *********
>
> **********************************************************************
> *********
>
> **
> **
> ** ##### ##
> ## **
> ** ## ## ## ##
> ## **
> ** ## ## ##
> ###### **
> ** ## ## ## ## ## ##### ## ## #### ## #####
> ##### **
> ** ## ## ## ## ## ## ## ## ## ## ## ##
> ## ## **
> ** ## ## ## ## ## ## ## #### ### ## ######
> ###### **
> ** ## ### ## ## ## ## ## ## ## ## ##
> ## **
> ** ####### ##### ## ##### ## ## #### ## #####
> ## **
> ** ##
> ## **
>
> **
> **
> ** ... make the atoms
> dance **
>
> **
> **
> ** Copyright (C) by CP2K Developers Group (2000 -
> 2008) **
>
> **
> **
>
> **********************************************************************
> *********
>
>
> SCF PARAMETERS Density
> guess: ATOMIC
>
> --------------------------------------------------------
>
> max_scf: 40
>
> max_scf_history: 0
>
> max_diis: 4
>
> --------------------------------------------------------
>
> eps_scf: 1.00E-05
>
> eps_scf_history: 0.00E+00
>
> eps_diis: 1.00E-01
>
> eps_eigval: 1.00E-05
>
> eps_jacobi: 0.00E+00
>
> jacobi_threshold: 1.00E-07
>
> --------------------------------------------------------
>
> p_mix: 0.40
> G-space mixing
> a: 1.00
> G-space mixing
> b: 0.00
>
> work_syevx: 1.00
> level_shift
> [a.u.]: 0.00
> smear
> [a.u.]: 0.00
> added
> MOs 0 0
>
> --------------------------------------------------------
> Outer loop SCF in use
> No variables optimised in outer loop
>
> eps_scf 1.00E-05
>
> max_scf 5
> No outer loop optimization
>
> step_size 5.00E-01
>
> 2D_MC| Monte Carlo annealing to optimize the distribution_2d
> 2D_MC| Number of
> moves 400000
> 2D_MC| Number of annealing
> cycles 10
> 2D_MC| Number of reduction steps per
> cycle 5
> 2D_MC| Reduction factor per step
> 0.8000000000
> 2D_MC| Termination tolerance
> 0.0200000000
> 2D_MC| Maximum temperature
> 0.5000000000
> 2D_MC| Swap probability
> 0.9000000000
> 2D_MC| Number of processor
> rows 4
> 2D_MC| Number of processor
> cols 4
> 2D_MC| Number of
> elements 150
> 2D_MC| Cost of optimal
> distribution 172157
> 2D_MC| Cost of found
> distribution 174861
> 2D_MC| Difference in
> percent 2
>
> Number of electrons: 414
> Number of occupied orbitals: 207
> Number of orbital functions: 2338
>
> Number of independent orbital functions: 2338
>
> Extrapolation method: initial_guess
>
>
> SCF WAVEFUNCTION OPTIMIZATION
>
> Step Update method Time Convergence
> Total energy
>
> ----------------------------------------------------------------------
> -------
>
> ----------------------------------- OT
> --------------------------------------
>
> Allowing for rotations: F
> minimizer : CG : conjugate gradient
> preconditioner : FULL_SINGLE_INVERSE : cholesky inversion of H + eS
> line search : 2PNT : 2 energies, one gradient
> stepsize : 0.15000000
> energy_gap : 0.20000000
> eps_taylor : 0.10000E-15
> max_taylor : 4
>
> ----------------------------------- OT
> --------------------------------------
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 13
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 14
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 12
> CP2K| condition FAILED at line 1459
> CP2K| Abnormal program termination, stopped by process number 8
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 9
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 7
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 4
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 6
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 1
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 3
> CP2K| condition FAILED at line 1472
> CP2K| Abnormal program termination, stopped by process number 2
> 7 processes killed (possibly by Open MPI)
> Job /cineca/sysprod/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/
> openmpi_wrapper ./cp2k.popt prot_6_2103.inp
>
>
> >
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